Noncoding RNAs in the Regulation of Pluripotency and Reprogramming

Noncanonical function of DGCR8 controls mESC exit from pluripotency

(2017) Daniel Cirera-Salinas et al.   JOURNAL OF CELL BIOLOGY

Significant differences of function and expression of microRNAs between ground state and serum-cultured pluripotent stem cells

(2017) Ying Yan et al.   Journal of Genetics and Genomics

miR-6539 is a novel mediator of somatic cell reprogramming that represses the translation of Dnmt3b

(2017) Fujia WU et al.   JOURNAL OF REPRODUCTION AND DEVELOPMENT

Inhibition of miRNA-212/132 improves the reprogramming of fibroblasts into induced pluripotent stem cells by de-repressing important epigenetic remodelling factors

(2017) Nils Pfaff et al.   Stem Cell Research

Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells

(2017) Vladimir V. Sherstyuk et al.   Scientific Reports

AK048794 maintains the mouse embryonic stem cell pluripotency by functioning as an miRNA sponge for miR-592

(2016) Y. Zhou et al.   BIOCHEMICAL JOURNAL

MiR-134-Mbd3 axis regulates the induction of pluripotency

(2016) Lei Zhang et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Pairing beyond the Seed Supports MicroRNA Targeting Specificity

(2016) James P. Broughton et al.   MOLECULAR CELL

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

(2016) Georges St. Laurent et al.   NUCLEIC ACIDS RESEARCH

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

H/ACA Box Small Nucleolar RNA 7A Promotes the Self-Renewal of Human Umbilical Cord Mesenchymal Stem Cells

(2016) Yan Zhang et al.   STEM CELLS

The Trans-Spliced Long Noncoding RNA tsRMST Impedes Human Embryonic Stem Cell Differentiation Through WNT5A-Mediated Inhibition of the Epithelial-to-Mesenchymal Transition

(2016) Chun-Ying Yu et al.   STEM CELLS

Maintenance of Self-Renewal and Pluripotency in J1 Mouse Embryonic Stem Cells through Regulating Transcription Factor and MicroRNA Expression Induced by PD0325901

(2016) Zhiying Ai et al.   Stem Cells International

MiR-31/SDHA Axis Regulates Reprogramming Efficiency through Mitochondrial Metabolism

(2016) Man Ryul Lee et al.   Stem Cell Reports

Efficient CRISPR/Cas9-Mediated Versatile, Predictable, and Donor-Free Gene Knockout in Human Pluripotent Stem Cells

(2016) Zhongliang Liu et al.   Stem Cell Reports

MicroRNA-Offset RNA Alters Gene Expression and Cell Proliferation

(2016) Jin Zhao et al.   PLoS One

Distinct MicroRNA Expression Signatures of Porcine Induced Pluripotent Stem Cells under Mouse and Human ESC Culture Conditions

(2016) Wei Zhang et al.   PLoS One

CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo

(2016) Hong Chang et al.   Scientific Reports

Using artificial microRNA sponges to achieve microRNA loss-of-function in cancer cells

(2015) Felix Chang Tay et al.   ADVANCED DRUG DELIVERY REVIEWS

Ribosomal profiling adds new coding sequences to the proteome

(2015) M. A. S. Mumtaz et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Re-thinking miRNA-mRNA interactions: Intertwining issues confound target discovery

(2015) Nicole Cloonan   BIOESSAYS

Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells

(2015) Anyou Wang et al.   BMC GENOMICS

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency

(2015) Y. Cao et al.   EMBO JOURNAL

Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells

(2015) Zhidong Yuan et al.   GENE

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

(2015) Jens Durruthy-Durruthy et al.   NATURE GENETICS

Brief Report: Inhibition of miR-145 Enhances Reprogramming of Human Dermal Fibroblasts to Induced Pluripotent Stem Cells

(2015) Tomas Barta et al.   STEM CELLS

GSK3 inhibitors CHIR99021 and 6-bromoindirubin-3′-oxime inhibit microRNA maturation in mouse embryonic stem cells

(2015) Yongyan Wu et al.   Scientific Reports

The emerging landscape of small nucleolar RNAs in cell biology

(2015) Fabien Dupuis-Sandoval et al.   Wiley Interdisciplinary Reviews-RNA

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l

(2015) Chryssa Kanellopoulou et al.   Stem Cell Reports

Canonical MicroRNA Activity Facilitates but May Be Dispensable for Transcription Factor-Mediated Reprogramming

(2015) Zhong Liu et al.   Stem Cell Reports

Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells

(2015) Suvi Asikainen et al.   PLoS One

The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues

(2015) Lukasz Michal Szafron et al.   PLoS One

Embryonic MicroRNA-369 Controls Metabolic Splicing Factors and Urges Cellular Reprograming

(2015) Masamitsu Konno et al.   PLoS One

Functional screen reveals essential roles of miR-27a/24 in differentiation of embryonic stem cells

(2014) Y. Ma et al.   EMBO JOURNAL

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

(2014) Patrick Essletzbichler et al.   GENOME RESEARCH

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

Genome-wide characterization of the routes to pluripotency

(2014) Samer M. I. Hussein et al.   NATURE

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

5′ isomiR variation is of functional and evolutionary importance

(2014) Geok Chin Tan et al.   NUCLEIC ACIDS RESEARCH

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

(2014) Andreas J. Gruber et al.   NUCLEIC ACIDS RESEARCH

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

(2014) Tsui-Ting Ho et al.   NUCLEIC ACIDS RESEARCH

Human Fibroblast Reprogramming to Pluripotent Stem Cells Regulated by the miR19a/b-PTEN Axis

(2014) Xiaoping He et al.   PLoS One

Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9

(2014) Jinxiong Han et al.   RNA Biology

sRNA-seq Analysis of Human Embryonic Stem Cells and Definitive Endoderm Reveals Differentially Expressed MicroRNAs and Novel IsomiRs with Distinct Targets

(2014) Andrew Hinton et al.   STEM CELLS

Small RNA changes en route to distinct cellular states of induced pluripotency

(2014) Jennifer L. Clancy et al.   Nature Communications

Understanding functional miRNA–target interactions in vivo by site-specific genome engineering

(2014) Andrew R. Bassett et al.   Nature Communications

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells

(2014) Yick W Fong et al.   eLife

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

(2014) Yul W Yang et al.   eLife

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

The let-7/LIN-41 Pathway Regulates Reprogramming to Human Induced Pluripotent Stem Cells by Controlling Expression of Prodifferentiation Genes

(2013) Kathleen A. Worringer et al.   Cell Stem Cell

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

(2013) C.-S. Wu et al.   GENOME RESEARCH

MicroRNA-based discovery of barriers to dedifferentiation of fibroblasts to pluripotent stem cells

(2013) Robert L Judson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Critical regulation of miR-200/ZEB2 pathway in Oct4/Sox2-induced mesenchymal-to-epithelial transition and induced pluripotent stem cell generation

(2013) G. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of pluripotency-associated microRNAs in rabbit preimplantation embryos and embryonic stem-like cells

(2013) Pouneh Maraghechi et al.   REPRODUCTION

Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds

(2013) P. Hou et al.   SCIENCE

HIF1α Modulates Cell Fate Reprogramming Through Early Glycolytic Shift and Upregulation of PDK1-3 and PKM2

(2013) Alessandro Prigione et al.   STEM CELLS

Dissecting the Roles of miR-302/367 Cluster in Cellular Reprogramming Using TALE-based Repressor and TALEN

(2013) Zhonghui Zhang et al.   Stem Cell Reports

microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming

(2012) Xudong Guo et al.   CELL RESEARCH

The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage

(2012) Ali Zhang et al.   CELL RESEARCH

Metabolic Regulation in Pluripotent Stem Cells during Reprogramming and Self-Renewal

(2012) Jin Zhang et al.   Cell Stem Cell

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation

(2012) Konstantinia Skreka et al.   NUCLEIC ACIDS RESEARCH

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

MiR-138 Promotes Induced Pluripotent Stem Cell Generation Through the Regulation of the p53 Signaling

(2012) Dan Ye et al.   STEM CELLS

MicroRNA-302 Increases Reprogramming Efficiency via Repression of NR2F2

(2012) Shijun Hu et al.   STEM CELLS

Nuclear Reprogramming with c-Myc Potentiates Glycolytic Capacity of Derived Induced Pluripotent Stem Cells

(2012) Clifford D. L. Folmes et al.   Journal of Cardiovascular Translational Research

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains

(2012) Le Cong et al.   Nature Communications

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

(2011) Athanasia D Panopoulos et al.   CELL RESEARCH

Highly Efficient miRNA-Mediated Reprogramming of Mouse and Human Somatic Cells to Pluripotency

(2011) Frederick Anokye-Danso et al.   Cell Stem Cell

Reprogramming of Mouse and Human Cells to Pluripotency Using Mature MicroRNAs

(2011) Norikatsu Miyoshi et al.   Cell Stem Cell

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Small RNA-mediated regulation of iPS cell generation

(2011) Zhonghan Li et al.   EMBO JOURNAL

MicroRNA Cluster 302–367 Enhances Somatic Cell Reprogramming by Accelerating a Mesenchymal-to-Epithelial Transition

(2011) Baojian Liao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells

(2011) Deepa Subramanyam et al.   NATURE BIOTECHNOLOGY

Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation

(2011) Jason Wray et al.   NATURE CELL BIOLOGY

miR-34 miRNAs provide a barrier for somatic cell reprogramming

(2011) Yong Jin Choi et al.   NATURE CELL BIOLOGY

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Methods for making induced pluripotent stem cells: reprogramming à la carte

(2011) Federico González et al.   NATURE REVIEWS GENETICS

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

(2011) Anthony K L Leung et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles

(2011) A. Jouneau et al.   RNA

microRNAs modulate iPS cell generation

(2011) C.-S. Yang et al.   RNA

A Latent Pro-Survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells

(2011) Grace X. Y. Zheng et al.   PLoS Genetics

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

(2011) Nicole Cloonan et al.   GENOME BIOLOGY

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

microRNAs regulate human embryonic stem cell division

(2010) Junlin Qi et al.   CELL CYCLE

A Mesenchymal-to-Epithelial Transition Initiates and Is Required for the Nuclear Reprogramming of Mouse Fibroblasts

(2010) Ronghui Li et al.   Cell Stem Cell

Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming

(2010) Payman Samavarchi-Tehrani et al.   Cell Stem Cell

Computational identification and characterization of primate-specific microRNAs in human genome

(2010) Sheng Lin et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production

(2010) Keita Miyoshi et al.   MOLECULAR GENETICS AND GENOMICS

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

(2010) Matthias Stadtfeld et al.   NATURE

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

(2010) Markus Brameier et al.   NUCLEIC ACIDS RESEARCH

Evidence for human microRNA-offset RNAs in small RNA sequencing data

(2009) D. Langenberger et al.   BIOINFORMATICS

MicroRNA-145 Regulates OCT4, SOX2, and KLF4 and Represses Pluripotency in Human Embryonic Stem Cells

(2009) Na Xu et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

iPS Cells Can Support Full-Term Development of Tetraploid Blastocyst-Complemented Embryos

(2009) Lan Kang et al.   Cell Stem Cell

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

Survey of Computational Algorithms for MicroRNA Target Prediction

(2009) Dong Yue et al.   CURRENT GENOMICS

Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo

(2009) J. Nichols et al.   DEVELOPMENT

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Embryonic stem cell–specific microRNAs promote induced pluripotency

(2009) Robert L Judson et al.   NATURE BIOTECHNOLOGY

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

(2009) Lorena Pantano et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

(2009) J. Sheik Mohamed et al.   RNA

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs

(2008) J. E. Babiarz et al.   GENES & DEVELOPMENT

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

The miR-200 Family Inhibits Epithelial-Mesenchymal Transition and Cancer Cell Migration by Direct Targeting of E-cadherin Transcriptional RepressorsZEB1andZEB2

(2008) Manav Korpal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1

(2008) Philip A. Gregory et al.   NATURE CELL BIOLOGY

Embryonic stem cell–specific microRNAs regulate the G1-S transition and promote rapid proliferation

(2008) Yangming Wang et al.   NATURE GENETICS

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells

(2008) Lasse Sinkkonen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state

(2008) S.-L. Lin et al.   RNA

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence

(2008) Louise C. Laurent et al.   STEM CELLS

MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries

(2008) Merav Bar et al.   STEM CELLS

Promotion of Reprogramming to Ground State Pluripotency by Signal Inhibition

(2008) Jose Silva et al.   PLOS BIOLOGY

Experimental validation of miRNA targets

(2007) Donald E. Kuhn et al.   METHODS

Inhibition of microRNA with antisense oligonucleotides

(2007) Christine C. Esau   METHODS